Polycistronic Vector for Human Induced Pluripotent Stem Cell Production

ABSTRACT

Methods of producing induced pluripotent stem (iPS) cells are provided. For example, a method of producing an iPS cell from a differentiated cell, which includes transforming the differentiated cell with a first vector comprising a nucleic acid sequence comprising a nucleic acid sequence encoding an Oct4, a nucleic acid sequence encoding a Sox2, and a nucleic acid sequence encoding a Klf4. Each of the nucleic acid sequences are separated from each other by a first and second viral 2A sequence. The method described can further comprise culturing the transformed cell under conditions that allow for the production of an iPS cell and isolating the cultured iPS cell.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.13/480,753, filed May 25, 2012, which is a divisional of U.S.application Ser. No. 12/640,767, filed Dec. 17, 2009, which claims thebenefit of U.S. Provisional Application No. 61/138,260, filed on Dec.17, 2008, all of which are incorporated herein in their entireties bythis reference.

STATEMENT REGARDING FEDERALLY FUNDED RESEARCH

This invention was made with government support under Grant No.RO1-HL057619 from the National Institutes of Health. The United Statesgovernment has certain rights in this invention.

BACKGROUND

Embryonic stem (ES) cells have the ability to grow indefinitely whilemaintaining pluripotency and the ability to differentiate into amultitude of different cell types. Because of these two qualities, humanES cell therapies have been proposed for regenerative medicine andtissue replacement after injury or disease. However, there are ethicaldifficulties regarding the use of human embryos for the isolation ofhuman ES cells as well as problems with tissue rejection followingtransplantation of foreign ES cells in patients.

SUMMARY

Methods of producing induced pluripotent stem (iPS) cells are provided.For example, methods of producing an iPS cell from a differentiated cellare provided. The methods include the step of transforming thedifferentiated cell with a first vector comprising a nucleic acidsequence comprising a nucleic acid sequence encoding an Oct4, a nucleicacid sequence encoding a Sox2, and a nucleic acid sequence encoding aKlf4. Each of the nucleic acid sequences are separated by a first andsecond nucleic acid sequence encoding a viral 2A sequence.

Also provided are methods of producing an iPS cell, wherein the vectorused to produce the cell is deleted from the genome of the iPS cell. Forexample, the methods include the step of transforming the differentiatedcell with a first vector comprising a nucleic acid sequence comprising anucleic acid sequence encoding an Oct4, a nucleic acid sequence encodinga Sox2, and a nucleic acid sequence encoding a Klf4. Each of the nucleicacid sequences are separated by a first and second nucleic acid sequenceencoding a viral 2A sequence. The vector further comprises a loxPsequence. The methods further include the step of transforming the iPScell with a second vector. The second vector comprises a nucleic acidsequence encoding a Cre recombinase. Expression of the Cre recombinaseresults in the deletion of the first retroviral vector from the genomeof the cells.

Also provided are vectors comprising a nucleic acid sequence encoding anOct4, a nucleic acid sequence encoding a Sox2, and a nucleic acidsequence encoding a Klf4, and cells comprising the vector. Each of thenucleic acid sequences are separated from each other by a first andsecond nucleic acid sequence encoding a viral 2A sequence.

Also provided are kits comprising a first vector and a second vector.The first vector comprises a nucleic acid sequence encoding an Oct4, anucleic acid sequence encoding a Sox2, and a nucleic acid sequenceencoding a Klf4. Each of the nucleic acid sequences are separated fromeach other by a first and second viral 2A sequence. The second vectorcomprises a nucleic acid sequence encoding a Cre recombinase.

Further provided are methods of treating or preventing a diseaseassociated with a genetic mutation in a subject. The methods compriseselecting a subject with a disease associated with a genetic mutation;isolating differentiated cells from the subject; transforming thedifferentiated cells with a vector comprising an unmutated nucleic acidsequence of interest; culturing the transformed cells under conditionsthat allow for the production of a population of iPS cells; screeningthe iPS cells for correction of the genetic mutation; and administeringthe iPS cells to the subject, wherein administration of the iPS cellstreats or prevents the disease associated with the genetic mutation inthe subject. The vector comprises a nucleic acid sequence comprising (i)an unmutated nucleic acid sequence of interest and homologous nucleicacid sequences flanking the genetic mutation, (ii) a nucleic acidsequence encoding a Cre recombinase operably linked to an induciblepromoter, (iii) a first and second loxP sequence, (iv) a nucleic acidsequence encoding an Oct4, (v) a nucleic acid sequence encoding a Sox2,and (vi) a nucleic acid sequence encoding a Klf4. Each of the nucleicacid sequences, (iv)-(vi), are separated by a first and second nucleicacid sequence encoding a viral 2A sequence.

DESCRIPTION OF DRAWINGS

FIGS. 1A and 1B show the Oct4, Sox2, Klf4 (OSK) lentiviral vector forreprogramming adult skin fibroblasts to iPS cells. FIG. 1A shows adiagram of the vector. FIG. 1B shows the amino acid sequence of the 2Apolypeptide with a 3-amino acid GSG linker (SEQ ID NO:1)

FIGS. 2A and 2B show images of iPS cell colonies. FIG. 2A showsimmunofluorescent images of iPS cell colonies stained for Nanog andSSEA1 expression. FIG. 2B shows images of iPS cell colonies stained foralkaline phosphatase expression with iPS-1 Cre1 representing a typicalcolony after Cre recombinase mediated deletion of the OSK vector.

FIGS. 3A and 3B show RT-PCR analysis and Bisulfite sequence analysis ofisolated iPS cells. FIG. 3A shows a gel of RT-PCR assays ofpolycistronic OSK RNA and endogenous Oct4, Sox2, Klf4, Nanog and CriptoRNA in iPS cells from 3 independent colonies (iPS-1, iPS-2, and iPS-3)and from iPS-1 cells post Cre recombinase mediated deletion of the OSKlentiviral vector (iPS-1 Cre1). FIG. 3B shows bisulfite sequencing ofthe endogenous and Oct4 and Nanog promoters in iPS-1, iPS-2, and iPS-1Cre1 cells. Filled circles represent methylated CpGs and open circlesrepresent unmethylated CpGs.

FIGS. 4A and 4B show a vector map and Southern blot hybridization ofiPS-1 cellular DNA. FIG. 4A shows a map of the OSK vector pre- andpost-Cre expression. K represents KpnI cleavage sites. The probe bindingsite is shown. FIG. 4B shows a Southern Blot demonstrating that iPS-1cells contain 4 copies of the OSK lentiviral vector, and iPS-1 Cre1cells contain no copies of the vector after transient Cre expression.

FIGS. 5A-5C show teratomas and chimeras derived from iPS cells. FIG. 5Ashows teratomas containing tissue derived from all three germ layers inNOD/SCID IL-2 γR−/−mice injected with isolated iPS cells. a,intestine-like epithelium, with pancreatic acini in iPS-3 teratoma; b,respiratory epithelium; c, skeletal muscle; d, bone, with hyalinecartilage in iPS-2 teratoma; e, nervous tissue; f, skin-like stratifiedsquamous epithelium. FIG. 5B shows chimeric embryos that were obtainedfollowing injection of iPS-1 Cre1 and iPS-1 Cre2 cells into wild typeblastocysts. The top panel is a gel showing PCR products demonstratingchimeric embryos as iPS cells contain the human β-globin gene as amarker. FIG. 5C shows an adult chimeric animal (right) compared to anadult non-chimeric littermate (left).

FIGS. 6A and 6B show a vector map and Southern blot hybridization ofiPS-1 and iPS-2 cellular DNA after OSK vector deletion. FIG. 6A shows amap of the OSK vector pre- and post-Cre expression. The probe bindingsite is shown. FIG. 6B shows a Southern blot demonstrating that iPS-1Cre cells contain 4 insertion sites and iPS-2 Cre cells contain 3insertion sites.

FIGS. 7A-G show the nucleotide (SEQ ID NO:7 for top strand and SEQ IDNO:8 for bottom strand) and amino acid (SEQ ID NO:9) sequences of thepolycistron encoded by the vector. Underlined and labeled are primersused to create the polycistron. The Oct4, Sox2, Klf4 and PTV1 2Asequences are denoted.

FIG. 8 shows a brightfield image of an iPS cell colony derived fromhuman keratinocytes using a polycistronic lentiviral vector.

FIG. 9 shows a schematic of a method to correct a β-globin mutationfound in sickle cell disease with concomitant formation of iPS cells.The β^(s)-globin locus is depicted at the top of the figure. Theβ^(s)-globin locus has a single nucleotide, A to T transversion in thefirst exon. The targeting vector is depicted in the middle of thefigure. The vector contains the normal GAG codon in the first exonflanked by sequences to effect homologous recombination. A herpessimplex virus thymidine kinase (HSV tk) gene is located outside of thesequences used to effect homologous recombination. Integrated betweenthe homology arms is a floxed cassette (loxP site on either side ofcassette) consisting of a Nanog-responsive (NBS) thymidine kinase (TK)promoter driving expression of Cre recombinase and the EF1α promoterdriving expression of the Oct4-Sox2-Klf4 polycistronic sequence. Thedashed lines show where the homologous recombination occurs. Afterhomologous recombination occurs, the endogenous Nanog gene is expressed.Nanog binds to the NBS sites and forces Cre recombinase expression. Crerecombinase excises the floxed cassette and leaves behind a correctβ-globin locus with a single loxP site in between exons 2 and 3 ofβ-globin.

DETAILED DESCRIPTION

A number of studies have been published detailing the production ofinduced pluripotent stem (iPS) cells from differentiated, embryonic andadult, mammalian cells (Takahashi and Yamanaka, Cell 1126:663-76 (2006);Meissner et al., Nat. Biotech. 25(10):1177-81 (2007); Takahashi et al.,Cell 131:861-72 (2007); and Park et al., Nature 451:141-7 (2008)). Ineach of these publications, four transcription factors, Oct-3/4, Sox2,Klf4, and c-Myc, were introduced to the differentiated cells throughretroviral transduction to produce iPS cells from differentiated somaticcells. Alternatively, it was found that another combination of factors,which include Oct-3/4, Sox2, Nanog, and Lin28, were capable ofreprogramming somatic cells to iPS cells that exhibit the essentialcharacteristics of embryonic stem (ES) cells (Yu et al., Science18:1917-20 (2007)).

Oct4 and Sox2 are core transcription factors that function in themaintenance of pluripotency in early embryos and embryonic stem (ES)cells (Nichols et al., Cell 95:379-391 (1998); Niwa et al., Nat. Genet.24:372-6 (2000); and Avilion et al., Gene Dev. 17:126-40 (2003)). Klf4has been shown to contribute to the long-term maintenance of the ES cellphenotype and the rapid proliferation of ES cells in culture (Li et al.,Blood 105:635-7 (2005)). Nanog is a transcription factor that isimportant in early development and stem cell pluripotency as itactivates ES cell critical factors and repressesdifferentiation-promoting genes (Wang et al., Proc. Natl. Acad. Sci. USA105:6326-31 (2008)). Lin28 is a marker of undifferentiated humanembryonic stem cells and has been shown to bind mRNAs in the cytoplasmas well as block the production of mature let-7 microRNA in mouseembryonic stem cells (Balzer and Moss, RNA Biology 4:16-25 (2007);Viswanathan et al., Science 320:97-100 (2008)). The c-Myc protein isalso a transcription factor, as well as a tumor-related factor, and hasmany targets that enhance proliferation and transformation (Adhikary andEilers, Nat. Rev. Mol. Cell. Bio. 6:635-45 (2005)) with many of thesedownstream targets potentially having roles in the generation of iPScells. Additionally, c-Myc may globally induce histone acetylation(Fernandez et al., Genes Dev. 17:1115-29 (2003)), to allow othertranscription factors to bind to their specific target loci. In the caseof iPS cell production, expression of c-Myc would result in histoneacetylation, thus allowing Oct3/4 and Sox2 to target the genes necessaryto create a stem cell-like cell.

The use of retroviruses to incorporate Oct3/4, Sox2, Klf4, and c-Mycinto the cells is both advantageous and deleterious. The advantages ofusing a retrovirus is that the virus integrates into the genome of thecell and thus is genetically transferred to the progeny when the cellundergoes cell division. This allows for the continued expression ofthese factors as differentiated cells undergo the transition to an iPScell. In spite of these advantages, Takahashi et al. found that each iPSclone contained three to six retroviral integrations for each factor,creating the possibility of more than 20 retroviral integration sitesper iPS clone, which increases the risk of tumorigenesis (Takahashi etal., Cell 131:861-72 (2007)). In fact, approximately 20% of mice derivedfrom iPS cells developed tumors. This was attributable, at least inpart, to the reactivation of the c-Myc retrovirus (Okita et al., Nature448:313-7 (2007)).

The methods and compositions provided herein are designed to produce iPScells that reduce the risk of insertional mutagenesis by allowing forthe removal or deletion of vectors once the iPS cells have beengenerated or by using vectors that do not integrate into the cellulargenome.

As used herein, the term induced pluripotent stem (iPS) cell encompassesany cell that has been reprogrammed to phenotypically resemble apluripotent stem cell. An iPS cell is derived from a non-pluripotentcell but is capable of reproducing itself. An iPS cell is also capableof terminal differentiation into a cell-type normally found in therelevant system, tissue, or organ. An iPS cell is similar to an ES cellin morphology, proliferation, and pluripotency. For example, an iPS celland an ES cell express the same markers. Examples of these markersinclude Oct3/4, Nanog, E-Ras, Cripto, Dax1, Fgf4, stage-specificembryonic antigen 1 (SSEA1), SSEA3, SSEA4, alkaline phosphatase,tumor-related antigen (TRA)-1-60, TRA-1-81, and Zfp296.

Provided herein are vectors for producing iPS cells. Thus, providedherein is a first vector comprising a nucleic acid sequence encoding anOct4, a nucleic acid sequence encoding a Sox2, and a nucleic acidsequence encoding a Klf4. Each of the nucleic acid sequences areseparated by a first and second nucleic acid sequence encoding a viral2A sequence. The first nucleic acid sequence encoding a viral 2Asequence is the same as or different from the second nucleic acidsequence encoding a viral 2A sequence. Optionally, the first vectorcomprises SEQ ID NO:7. Optionally, the first vector comprises a nucleicacid sequence encoding SEQ ID NO:9. Optionally, the first vectorcomprises SEQ ID NO:43. The vector comprising SEQ ID NO:43 was depositedwith the American Type Culture Collection, 10801 University Boulevard,Manassas, Va. 20110-2209 in accordance with the Budapest Treaty on Oct.6, 2009, and has accession number PTA-10385.

Optionally, Oct4, Sox2, and Klf4 are human. Optionally, Oct4, Sox2, andKlf4 are non-human (e.g., rodent, canine, or feline). There are avariety of sequences that are disclosed on Genbank, at www.pubmed.govand these sequences and others are herein incorporated by reference intheir entireties as are individual subsequences or fragments containedtherein. As used herein, Oct4 refers to the Oct4 transcription factorand homologs, variants, and isoforms thereof. For example, thenucleotide and amino acid sequences of human Oct4 can be found atGenBank Accession Nos. BC 117435 and AAI17436.1, respectively.Optionally, the nucleotide and amino acid sequences of human Oct4isoform 1 can be found at GenBank Accession Nos. NM_(—)002701.4 andNP_(—)002692.2, respectively. The nucleotide and amino acid sequencesfor human Oct4 isoform 2 can be found at GenBank Accession Nos.NM_(—)203289.3 and NP_(—)976034.3, respectively. As used herein, Sox2refers to the Sox2 transcription factor and homologs, variants, andisoforms thereof. The nucleotide and amino acid sequences of human Sox2can be found at GenBank Accession Nos. BC013923 and AAH13923.1,respectively. Optionally, the nucleotide and amino acid sequences ofhuman Sox2 can be found at GenBank Accession Nos. NM_(—)003106.2 andNP_(—)003097.1, respectively. As used herein, Klf4 refers to the Klf4transcription factor and homologs, variants, and isoforms thereof. Thenucleotide and amino acid sequences of human Klf4 can be found atGenBank Accession Nos. BC029923 and AAH29923.1, respectively.Optionally, the nucleotide and amino acid sequences of human Klf4 can befound at GenBank Accession Nos. NM_(—)004235.4 and NP_(—)004226.3,respectively. Thus provided are the nucleotide sequences of Oct4, Sox2,and Klf4 comprising a nucleotide sequence at least about 70%, 75%, 80%,85%, 90%, 95%, 98%, 99% or more identical to the nucleotide sequence ofthe aforementioned GenBank Accession Numbers. Also provided are aminoacid sequences of Oct4, Sox2, and Klf4 comprising an amino acid sequenceat least about 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more identicalto the sequences of the aforementioned GenBank Accession Numbers.

Nucleic acids that encode the polypeptide sequences, variants, andfragments thereof are disclosed. These sequences include all degeneratesequences related to a specific protein sequence, i.e., all nucleicacids having a sequence that encodes one particular protein sequence aswell as all nucleic acids, including degenerate nucleic acids, encodingthe disclosed variants and derivatives of the protein sequences. Thus,while each particular nucleic acid sequence may not be written outherein, it is understood that each and every sequence is in factdisclosed and described herein through the disclosed protein sequences.

As used herein, the term peptide, polypeptide or protein is used to meana molecule comprised of two or more amino acids linked by a peptidebond. Protein, peptide, and polypeptide are also used hereininterchangeably to refer to amino acid sequences. It should berecognized that the term polypeptide or protein is not used herein tosuggest a particular size or number of amino acids comprising themolecule and that a polypeptide of the disclosure can contain up toseveral amino acid residues or more.

As with all peptides, polypeptides, and proteins, including fragmentsthereof, it is understood that additional modifications in the aminoacid sequence of the variant Oct4, Sox2, and Klf4 polypeptides can occurthat do not alter the nature or function of the peptides, polypeptides,or proteins. Such modifications include conservative amino acidssubstitutions and are discussed in greater detail below.

The polypeptides provided herein have a desired function. Oct4 and Sox2are core transcription factors that regulate the expression of a definedset of target genes to maintain the pluripotency associated with EScells. Klf4 is a transcription factor that regulates the expression of adefined set of target genes to maintain the long-term ES cell phenotypeas well as to drive the proliferation of ES cells. The polypeptides aretested for their desired activity using the in vitro assays describedherein.

The polypeptides described herein can be further modified and varied solong as the desired function is maintained. It is understood that oneway to define any known modifications and derivatives or those thatmight arise, of the disclosed genes and proteins herein is throughdefining the modifications and derivatives in terms of identity tospecific known sequences. Specifically disclosed are polypeptides whichhave at least 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83 ,84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 percentidentity to Oct4, Sox2, and Klf4 and variants provided herein. Those ofskill in the art readily understand how to determine the identity of twopolypeptides. For example, the identity can be calculated after aligningthe two sequences so that the identity is at its highest level.

Another way of calculating identity can be performed by publishedalgorithms. Optimal alignment of sequences for comparison may beconducted by the local identity algorithm of Smith and Waterman, Adv.Appl. Math 2:482 (1981), by the identity alignment algorithm ofNeedleman and Wunsch, J. Mol. Biol. 48:443 (1970), by the search forsimilarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. USA85:2444 (1988), by computerized implementations of these algorithms(GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics SoftwarePackage, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or byinspection.

The same types of identity can be obtained for nucleic acids by, forexample, the algorithms disclosed in Zuker, Science 244:48-52 (1989);Jaeger et al., Proc. Natl. Acad. Sci. USA 86:7706-10 (1989); Jaeger etal., Methods Enzymol. 183:281-306 (1989), which are herein incorporatedby reference for at least material related to nucleic acid alignment. Itis understood that any of the methods typically can be used and that incertain instances the results of these various methods may differ, butthe skilled artisan understands if identity is found with at least oneof these methods, the sequences would be said to have the statedidentity and to be disclosed herein.

Protein modifications include amino acid sequence modifications.Modifications in amino acid sequence may arise naturally as allelicvariations (e.g., due to genetic polymorphism), may arise due toenvironmental influence (e.g., by exposure to ultraviolet light), or maybe produced by human intervention (e.g., by mutagenesis of cloned DNAsequences), such as induced point, deletion, insertion, and substitutionmutants. These modifications can result in changes in the amino acidsequence, provide silent mutations, modify a restriction site, orprovide other specific mutations. Amino acid sequence modificationstypically fall into one or more of three classes: substitutional,insertional, or deletional modifications. Insertions include aminoand/or terminal fusions as well as intrasequence insertions of single ormultiple amino acid residues. Insertions ordinarily will be smallerinsertions than those of amino or carboxyl terminal fusions, forexample, on the order of one to four residues. Deletions arecharacterized by the removal of one or more amino acid residues from theprotein sequence. Typically, no more than about from 2 to 6 residues aredeleted at any one site within the protein molecule. Amino acidsubstitutions are typically of single residues, but can occur at anumber of different locations at once; insertions usually will be on theorder of about from 1 to 10 amino acid residues; and deletions willrange about from 1 to 30 residues. Deletions or insertions preferablyare made in adjacent pairs, i.e., a deletion of 2 residues or insertionof 2 residues. Substitutions, deletions, insertions or any combinationthereof may be combined to arrive at a final construct. The mutationsmust not place the sequence out of reading frame and preferably will notcreate complementary regions that could produce secondary mRNAstructure. Substitutional modifications are those in which at lease oneresidue has been removed and a different residues inserted in its place.Such substitutions generally are made in accordance with the followingTable 1 and are referred to as conservative substitutions.

TABLE 1 Amino Acid Substitutions Substitutions Amino Acid (others areknown in the art) Ala Ser, Gly, Cys Arg Lys, Gln, Met, Ile Asn Gln, His,Glu, Asp Asp Glu, Asn, Gln Cys Ser, Met, Thr Gln Asn, Lys, Glu, Asp GluAsp, Asn, Gln Gly Pro, Ala His Asn, Gln Ile Leu, Val, Met Leu Ile, Val,Met Lys Arg, Gln, Met, Ile Met Leu, Ile, Val Phe Met, Leu, Tyr, Trp, HisSer Thr, Met, Cys Thr Ser, Met, Val Trp Tyr, Phe Tyr Trp, Phe, His ValIle, Leu, Met

Modifications, including the specific amino acid substitutions, are madeby known methods. By way of example, modifications are made by sitespecific mutagenesis of nucleotides in the DNA encoding the protein,thereby producing DNA encoding the modification, and thereafterexpressing the DNA in recombinant cell culture. Techniques for makingsubstitution mutations at predetermined sites in DNA having a knownsequence are well known, for example M13 primer mutagenesis and PCRmutagenesis.

Optionally, the vector comprises its various components in any order.Examples include from the 5′ end, a nucleic acid sequence encoding afirst polypeptide, the first nucleic acid encoding a viral 2A sequence,a nucleic acid encoding a second polypeptide, the second nucleic acidsequence encoding a viral 2A sequence, and a nucleic acid sequenceencoding a third polypeptide. The first nucleic acid sequence encoding aviral 2A sequence is the same as or different from the second nucleicacid sequence encoding a viral 2A sequence. The first, second, and thirdpolypeptides are selected from the group consisting of Oct4, Sox2, andKlf4, and the first, second, and third polypeptides are different fromeach other. Thus, for example, the first polypeptide is Oct4, the secondpolypeptide is Sox2, and the third polypeptide is Klf4. By way ofanother example, the first polypeptide is Sox2, the second polypeptideis Oct4, and the third polypeptide is Klf4.

The vector comprises in order from the 5′ end, a nucleic acid sequenceencoding an Oct4, a first nucleic acid sequence encoding a viral 2Asequence, a nucleic acid sequence encoding a Sox2, a second nucleic acidsequence encoding a viral 2A sequence, and a nucleic acid sequenceencoding a Klf4. Optionally, the vector comprises in order from the 5′end, a nucleic acid sequence encoding an Oct4, a first nucleic acidsequence encoding a viral 2A sequence, a nucleic acid sequence encodinga Klf4, a second nucleic acid sequence encoding a viral 2A sequence, anda nucleic acid sequence encoding a Sox2. Optionally, the vectorcomprises in order from the 5′ end, a nucleic acid sequence encoding aSox2, a first nucleic acid sequence encoding a viral 2A sequence, anucleic acid sequence encoding an Oct4, a second nucleic acid sequenceencoding a viral 2A sequence, and a nucleic acid sequence encoding aKlf4. Optionally, the vector comprises in order from the 5′ end, anucleic acid sequence encoding a Sox2, a first nucleic acid sequenceencoding a viral 2A sequence, a nucleic acid sequence encoding a Klf4, asecond nucleic acid sequence encoding a viral 2A sequence, and a nucleicacid sequence encoding an Oct4. Optionally, the vector comprises inorder from the 5′ end, a nucleic acid sequence encoding a Klf4, a firstnucleic acid sequence encoding a viral 2A sequence, a nucleic acidsequence encoding an Oct4, a second nucleic acid sequence encoding aviral 2A sequence, and a nucleic acid sequence encoding a Sox2.Optionally, the vector comprises in order from the 5′ end, a nucleicacid sequence encoding a Klf4, a first nucleic acid sequence encoding aviral 2A sequence, a nucleic acid sequence encoding a Sox2, a secondnucleic acid sequence encoding a viral 2A sequence, and a nucleic acidsequence encoding an Oct4.

A common strategy of positive-strand RNA viruses is to encode some, orall, of their proteins in the form of a polyprotein translated from oneRNA molecule. Viruses have adapted multiple methods to allow for theproduction of individual protein molecules from a polyprotein. In thecase of picornaviruses, all of the proteins are encoded in a single openreading frame. The picornaviral polyproteins undergo a cleavage eventbetween the major domains of the viral genome, which are separated byviral 2A sequences. Viral 2A sequences allow for the translation ofmultiple polypeptides in a multicistronic RNA molecule by stimulatingpeptide cleavage between the polypeptides without disengaging theribosome. The use of viral 2A sequences to produce multiple proteinsfrom a multicistronic message is known, see, e.g., Donnelly et al., J.Gen. Virol. 82:1013-25 (2001); Donnelly et al., J. Gen. Virol.82:1027-41 (2001); Chinnasamy et al., Virol. J. 3:14 (2006); Holstetal., Nat. Protoc. 1(1):406-17 (2006); and Szymczak et al., Nat.Biotechnol. 22(5):589-94 (2004).

Optionally, the first and second nucleic acid sequences encoding a viral2A sequence is a picornaviral, a tetraviral 2A sequence, or acombination thereof. Optionally, the picornaviral 2A sequences areselected from the group consisting of the Enteroviral 2A sequences,Rhinoviral 2A sequences, Cardioviral 2A sequences, Aphthoviral 2Asequences, Hepatoviral 2A sequences, Erboviral 2A sequences, Kobuviral2A sequences, Teschoviral 2A sequences, and the Parechoviral 2Asequences. Optionally, the tetraviral 2A sequences are selected fromBetatetraviral 2A sequences or Omegatetraviral 2A sequences. Optionally,the first and second nucleic acid sequences encoding a viral 2A sequenceare picornaviral 2A sequences. Optionally, the first and second nucleicacid sequence encoding a viral 2A sequence is a Teschoviral 2A sequence.Optionally, the first nucleic acid sequence encoding a viral 2A sequenceis a Cardioviral 2A sequence, and the second nucleic acid sequenceencoding a viral 2A sequence is a Hepatoviral 2A sequence. Optionally,the first and second nucleic acid sequences encoding a viral 2A sequenceare tetraviridae 2A sequences. Optionally, the first and second nucleicacid sequences encoding a viral 2A sequence is a Betatetraviral 2Asequence. Optionally, the first nucleic acid sequence encoding a viral2A sequence is a Betatetraviral 2A sequence, and the second nucleic acidsequence encoding a viral 2A sequence is an Omegatetraviral 2A sequence.Optionally, the first nucleic acid sequence encoding a viral 2A sequenceis a picornaviral 2A sequence, and the second nucleic acid sequenceencoding a viral 2A sequence is a tetraviridae 2A sequence. Optionally,the first nucleic acid sequence encoding a viral 2A sequence is aTeschoviral 2A sequence, and the second nucleic acid sequence encoding aviral 2A sequence is a Betatetraviral 2A sequence. Optionally, the firstnucleic acid sequence encoding a viral 2A sequence is a tetraviridae 2Asequence, and the second nucleic acid sequence encoding a viral 2Asequence is a picornaviral 2A sequence. Optionally, the first nucleicacid sequence encoding a viral 2A sequence is a Betatetraviral 2Asequence, and the second nucleic acid sequence encoding a viral 2Asequence is a Teschoviral 2A sequence. Optionally, the first and secondnucleic acid sequences encoding a viral 2A sequence comprise a nucleicacid sequence encoding the amino acid sequence ATNFSLLKQAGDVEENPGP (SEQID NO:2). Optionally, the first and second nucleic acid sequencesencoding a viral 2A sequence comprise a nucleic acid sequence encodingthe amino acid sequence EGRGSLLTCGDVEENPGP (SEQ ID NO:3). Optionally thefirst nucleic acid sequence encoding a viral 2A sequence comprises anucleic acid sequence encoding the amino acid sequenceATNFSLLKQAGDVEENPGP (SEQ ID NO:2), and the second nucleic acid sequenceencoding a viral 2A sequence comprises a nucleic acid sequence encodingthe amino acid sequence EGRGSLLTCGDVEENPGP (SEQ ID NO:3).

Optionally the first and second nucleic acid sequences encoding a viral2A sequence comprises a nucleic acid sequence encoding an amino acidlinker. The amino acid linker can be 1 to 10 amino acids in length. Theamino acid linker can be 1 to 5 amino acids in length. The amino acidlinker can be 1 to 3 amino acids in length. The amino acid linker ispreferably 3 amino acids in length. The amino acid linker is, forexample, GSG (SEQ ID NO:4). Optionally the first and second nucleic acidsequences encoding a viral 2A sequence with an amino acid linkercomprise a nucleic acid sequence encoding the amino acid sequenceGSGATNFSLLKQAGDVEENPGP (SEQ ID NO:1). Optionally the first and secondnucleic acid sequences encoding a viral 2A sequence with an amino acidlinker comprise a nucleic acid sequence encoding the amino acid sequenceGSGEGRGSLLTCGDVEENPGP (SEQ ID NO:5).

The provided vector, for example, can be a retroviral vector. Retroviralvectors are able to integrate efficiently into the genomic DNA of cells.Integration into the genomic DNA allows for the continuous expression ofthe transgene and additionally allows for the transmission of thetransgene to progeny cells when the cells divide. Another advantage ofretroviral vectors is that they have the ability of being able totransduce a wide range of cell types from different animal species.Examples of retroviral vectors are known. See, e.g., Coffin et al.,Retorviruses, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y. (1997).

Optionally, the retroviral vector is a lentiviral vector. Lentiviralvectors are capable of infecting non-dividing cells. Optionally, thelentiviral vector is a lentiviral self-inactivating (SIN) vector.Lentiviral SIN vectors overcome the risk of activating cellularoncogenes when they are randomly integrated into the host genome. Thelentiviral SIN vector is generated by deleting viral enhancer andpromoter sequences within the vector, so that integration into thegenome does not result in the activation of cellular oncogenes driven bythe viral promoter and enhancer sequences. Methods of making and usingthe lentiviral SIN vectors are known. See, e.g., Miyoshi et al., J.Virol. 72(10):8150-7 (1998) and Zufferey et al., J. Virol.72(12):9873-80 (1998).

Optionally, the retroviral vector contains a loxP sequence (e.g.,ATAACTTCGTATAATGTATGCTATACGAAGTTAT (SEQ ID NO:6)). The loxP nucleic acidsequence is generally a 34 base pair nucleic acid sequence derived fromBacteriophage P1 that is used in combination with Cre recombinase toallow for site specific recombination. When a nucleic acid sequencecontains a loxP sequence, the location of the loxP sequence is referredto as a loxP site. Usually, a nucleic acid sequence contains two loxPsites. The loxP sites are located on either side of a nucleic acidsequence to be removed from, for example, the genome of a cell.Expression of Cre recombinase in the cell promotes a recombination eventthat results in the deletion of the genomic DNA that is present inbetween the loxP sites. Specifically, the Cre recombinase binds andcatalyzes the cleavage and strand exchange of DNA at two loxP sites,excising the nucleic acid between the loxP sites, and leaving a singleloxP site in the genome. Examples of the Cre/lox system are known. See,e.g., Sauer, Methods 14(4):381-92 (1998); Florin et al., Genesis38(3):139-44; and Schnutgen et al., Nat. Biotechnol. 21(5):562-5 (2003).

Optionally, the loxP sequence is located in the 3′ long terminal repeatof the vector. Retroviral integration into the genome of a cell occursin a three part process. First the retroviral RNA is reverse transcribedby a virally encoded RNA reverse transcriptase to form a RNA-DNA hybridhelix. The reverse transcriptase uses the newly synthesized DNA as atemplate to synthesize the complementary DNA, while degrading the RNAtemplate. The resulting DNA duplex is integrated into the genome of thecell with the loxP sequence in the 3′ long terminal repeat of theretroviral vector copied into the 5′ long terminal repeat during reversetranscription and then integrated into the genome. This provides a loxPsequence at either end of the integrated lentiviral vector; therefore,making it possible to remove the integrated retroviral vector byexpression of Cre recombinase. Optionally, provided is a second vectorcomprising a nucleic acid encoding a Cre recombinase. Expression of theCre recombinase results in the deletion of the first vector from thegenome of the iPS cells.

Optionally, the vector is designed to correct a genetic mutationassociated with a disease and to produce induced pluripotent stem (iPS)cells. The vector comprises a nucleic acid sequence comprising (i) anucleic acid sequence encoding an Oct4, (ii) a nucleic acid sequenceencoding a Sox2, and (iii) a nucleic acid sequence encoding a Klf4. Eachof the nucleic acid sequences, (i)-(iii), are separated by a first andsecond nucleic acid sequence encoding a viral 2A sequence. The firstnucleic acid sequence encoding a viral 2A sequence is the same as ordifferent from the second nucleic acid sequence encoding a viral 2Asequence. The vector further comprises an unmutated nucleic acidsequence of interest and homologous nucleic acid sequences flanking thegenetic mutation. An unmutated nucleic acid sequence of interest is anucleic acid sequence lacking the genetic mutation associated with thedisease. Optionally, the unmutated nucleic acid sequence of interestcomprises the nucleic acid sequence encoding β-globin. Optionally, thevector further comprises a first and second loxP sequence. Optionally,the vector further comprises a nucleic acid sequence encoding a Crerecombinase operably linked to an inducible promoter. The induciblepromoter, for example, can comprise a Nanog-responsive thymidine kinasepromoter. Optionally, the vector can comprise a selectable marker.Optionally, the vector comprises SEQ ID NO:44.

Optionally, the nucleic acid comprising a nucleic acid sequence encodingan Oct4, a nucleic acid sequence encoding a Sox2, and a nucleic acidsequence encoding a Klf4, wherein the nucleic acid sequences areseparated by a first and second nucleic acid sequence encoding a viral2A sequence is administered by another type of vector comprising thenucleic acid. The vector based delivery is largely broken down into twoclasses: viral based delivery systems and non-viral based deliverysystems. Such methods are known in the art and are readily adaptable foruse with the methods described herein.

Provided herein are viral based expression vectors comprising thedisclosed nucleic acid. Viral based delivery systems can, for example,include Adenoviral vectors, Adeno-associated viral vectors, Herpes viralvectors, Vaccinia viral vectors, Polio viral vectors, Sindbis viralvectors, and any other RNA viral vectors. Also useful are any viralfamilies that share the properties of these listed viruses and vectorsthat make them suitable for use as vectors. The construction ofreplication-defective adenoviruses has been described (Berkner et al.,J. Virology 61:1213-20 (1987); Massie et al., Mol. Cell. Biol. 6:2872-83(1986); Haj-Ahmad et al., J. Virology 57:267-74 (1986); Davidson et al.,J. Virology 61:1226-39 (1987); Zhang et al., BioTechniques 15:868-72(1993)). The viral vectors are limited in the extent to which they canspread to other cell types, since they can replicate within an initialinfected cell but are unable to form new infectious viral particles.Recombinant adenoviruses have been shown to achieve high efficiencyafter direct, in vivo delivery to airway epithelium, hepatocytes,vascular endothelium, CNS parenchyma and a number of other tissue sites.Other useful systems include, for example, replicating andhost-restricted non-replicating vaccinia virus vectors.

Provided herein are also non-viral based expression vectors comprisingthe disclosed nucleic acids. Suitable vector backbones include, forexample, plasmids, artificial chromosomes, BACs, YACs, or PACs. Numerousvectors and expression systems are commercially available from suchcorporations as Novagen (Madison, Wis.), Clonetech (Palo Alto, Calif.),Stratagene (La Jolla, Calif.), and Invitrogen/Life Technologies(Carlsbad, Calif.). Vectors typically contain one or more regulatoryregions. Regulatory regions include, without limitation, promotersequences, enhancer sequences, response elements, protein recognitionsites, inducible elements, protein binding sequences, 5′ and 3′untranslated regions (UTRs), transcriptional start sites, terminationsequences, polyadenylation sequences, and introns.

Any of the vectors provided herein can have a promoter sequence thatdrives the expression of the nucleic acid sequence comprising a nucleicacid sequence encoding a an Oct4, a nucleic acid sequence encoding aSox2, and a nucleic acid sequence encoding a Klf4. Each of the nucleicacid sequences are separated from each other by a first and second viral2A sequence. The first viral 2A sequence is the same as or differentfrom the second viral 2A sequence. Preferred promoters controllingtranscription from vectors in mammalian host cells may be obtained fromvarious sources, for example, the genomes of viruses such as polyoma,Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis B virus andmost preferably cytomegalovirus, or from heterologous mammalianpromoters, e.g. beta actin promoter or EF1 promoter, or from hybrid orchimeric promoters (e.g., cytomegalovirus promoter fused to the betaactin promoter). The early and late promoters of the SV40 virus areconveniently obtained as an SV40 restriction fragment which alsocontains the SV40 viral origin of replication. The immediate earlypromoter of the human cytomegalovirus is conveniently obtained as aHindIII E restriction fragment. Of course, promoters from the host cellor related species also are useful herein.

The promoter can be an inducible promoter (e.g. chemically or physicallyregulated promoter). A chemically regulated promoter can, for example,be regulated by the presence of alcohol, tetracycline, a steroid, or ametal. A physically regulated promoter can, for example, be regulated byenvironmental factors, such as temperature and light. The promoter canbe a cell type specific promoter (e.g. neuronal-specific,renal-specific, cardio-specific, liver-specific, or muscle-specific). Acell-type specific promoter is only expressed in the cell-type in whichit is intended to be expressed. The promoter can be a promoter that isexpressed independent of cell type. Examples of promoters that can beexpressed independent of cell type include the cytomegalovirus (CMV)promoter, the Raus sarcoma virus (RSV) promoter, the adenoviral E1Apromoter, and the EF-la promoter. The promoter is preferably the EF-lapromoter.

Enhancer generally refers to a sequence of DNA that functions at nofixed distance from the transcription start site and can be either 5′ or3′ to the transcription unit. Furthermore, enhancers can be within anintron as well as within the coding sequence itself. They are usuallybetween 10 and 300 base pairs in length, and they function in cis.Enhancers usually function to increase transcription from nearbypromoters. Enhancers can also contain response elements that mediate theregulation of transcription. While many enhancer sequences are now knownfrom mammalian genes (globin, elastase, albumin, fetoprotein andinsulin), typically one will use an enhancer from a eukaryotic cellvirus for general expression. Preferred examples are the SV40 enhanceron the late side of the replication origin, the cytomegalovirus earlypromoter enhancer, the polyoma enhancer on the late side of thereplication origin, and adenovirus enhancers.

The vectors also can include, for example, origins of replication,scaffold attachment regions (SARs), and/or markers. A marker gene canconfer a selectable phenotype, e.g., antibiotic resistance, on a cell.This marker product is used to determine if the gene has been deliveredto the cell and once delivered is being expressed. Examples of markergenes include the E. coli lacZ gene, which encodes B galactosidase,green fluorescent protein (GFP), and luciferase. Examples of suitableselectable markers for mammalian cells are dihydrofolate reductase(DHFR), thymidine kinase, neomycin, neomycin analog G418, hygromycin,blasticidin, and puromycin. When such selectable markers aresuccessfully transferred into a mammalian host cell, the transformedmammalian host cell can survive if placed under selective pressure. Inaddition, an expression vector can include a tag sequence designed tofacilitate manipulation or detection (e.g., purification orlocalization) of the expressed polypeptide. Tag sequences, such as greenfluorescent protein (GFP), glutathione S-transferase (GST),polyhistidine, c-myc, hemagglutinin, or FLAG™ tag (Kodak, New Haven,Conn.) sequences typically are expressed as a fusion with the encodedpolypeptide. Such tags can be inserted anywhere within the polypeptide,including at either the carboxyl or amino terminus.

Provided herein are methods for the production of iPS cells fromdifferentiated cells. The methods include transforming thedifferentiated cell with a first vector comprising a nucleic acidsequence comprising a nucleic acid sequence encoding an Oct4, a nucleicacid sequence encoding a Sox2, and a nucleic acid sequence encoding aKlf4. Each of the nucleic acid sequences are separated by a first andsecond nucleic acid sequence encoding a viral 2A sequence. The firstnucleic acid sequence encoding a viral 2A sequence can be the same as ordifferent from the second nucleic acid sequence encoding a viral 2Asequence. Optionally, the method further includes transforming thedifferentiated cell with a second vector comprising a nucleic acidsequence encoding a c-Myc. Optionally, the first vector comprises anucleic acid sequence comprising a nucleic acid sequence encoding anOct4, a nucleic acid sequence encoding a Sox2, a nucleic acid sequenceencoding a Klf4, and a nucleic acid sequence encoding a c-Myc. Each ofthe nucleic acid sequences are separated by a first, second, and thirdnucleic acid sequence encoding a viral 2A sequence. The first nucleicacid sequence encoding a viral 2A sequence can be the same as ordifferent from the second nucleic acid sequence encoding a viral 2Asequence. The second nucleic acid sequence encoding a viral 2A sequencecan be the same as or different from the third nucleic acid sequenceencoding a viral 2A sequence. Optionally, the first vector comprises anucleic acid sequence comprising a nucleic acid sequence encoding anOct4, a nucleic acid sequence encoding a Sox2, and a nucleic acidsequence encoding a Nanog, wherein the nucleic acid sequences are eachseparated by a first and second nucleic acid sequence encoding a viral2A sequence. The first nucleic acid sequence encoding a viral 2Asequence can be the same as or different from the second nucleic acidencoding a viral 2A sequence. The method further includes transformingthe differentiated cell with a second vector comprising a nucleic acidsequence encoding a Lin28. Optionally, the first vector comprises anucleic acid sequence comprising a nucleic acid sequence encoding anOct4, a nucleic acid sequence encoding a Sox2, a nucleic acid sequenceencoding a Nanog, and a nucleic acid sequence encoding a Lin28. Each ofthe nucleic acid sequences are separated by a first, second, and thirdnucleic acid sequence encoding a viral 2A sequence. The first nucleicacid sequence encoding a viral 2A sequence can be the same as ordifferent from the second nucleic acid sequence encoding a viral 2Asequence. The second nucleic acid sequence encoding a viral 2A sequencecan be the same as or different from the third nucleic acid sequenceencoding a viral 2A sequence.

As used herein, the term transforming is used broadly to define a methodof inserting a vector into a target cell. This can be accomplished, forexample, by transfecting the vector into a target cell. Transfecting avector into a target cell can be accomplished through the use ofcarriers, which can be divided into three primary classes: (cationic)polymers, liposomes, and nanoparticles. Examples of cationic polymersare DEAE-dextran and polyethylenimine, which bind the negatively chargedvector and allows for the vector to be taken up by the cell throughendocytosis. Liposomes are small, membrane-bounded bodies that fuse withthe cell membrane and allow for the release of the vector into the cell.Nanoparticles are coupled to the vector and are shot directly into thenucleus of a cell using a gene gun. Transfections can further be dividedinto two categories: stable and transient transfections. Stabletransfections result in the vector being permanently introduced into thecell and can be accomplished through the use of selectable marker, e.g.,antibiotic resistance, as discussed herein. Transient transfectionsresult in the vector being introduced temporarily to the cell.Alternatively, if the vector is a viral vector, it can be transfectedinto a host cell to produce virus, and the virus can be harvested andused to transduce the vector into the target cell. Transfection andtransduction protocols are known. See, e.g., Sambrook et al., MolecularCloning: A Laboratory Manual, 3^(rd) Ed., Cold Spring Harbor Press, ColdSpring Harbor, N.Y. (2001); Ausubel et al. (eds.), Current Protocols inMolecular Biology, John Wiley & Sons, Hoboken, N.J. (2004).

The differentiated cell can, for example, be obtained from a subject.The differentiated cell can be obtained and cultured from the subject bya variety of methods known and described, e.g., in Schantz and Ng, AManual for Primary Human Cell Culture, World Scientific, Hackensack,N.J. (2004); and Human Cell Culture Protocols 2^(nd) Edition, (Ed.Picot, J), Humana Press, Totowa, N.J. (2004).

Optionally, the differentiated cell is a mammalian cell. The mammaliancell is optionally a human cell. Mammalian cells suitable for use in theclaimed methods, include, but are not limited to epithelial cells,keratinocytes, fibroblasts, hepatocytes, neurons, osteoblasts, myocytes,kidney cells, lung cells, thyroid cells, and pancreatic cells.

Optionally, the methods further comprise culturing the transformed cellunder conditions that allow for the isolation of an iPS cell or apopulation of iPS cells. For example, transformed cells (e.g.,transformed keratinocytes) can be cultured under conditions withrelatively high calcium levels. Specifically, prior to transfection, thedifferentiated cells are cultured under conditions with low calciumlevels in the range of 0.01 mM to 0.1 mM. After transformation, thetransformed cells are cultured under conditions with high calcium levelsin the range of 1.0 mM to 2.0 mM. The high calcium levels promote thedeath of any untransformed differentiated cells but allow the survivalof transformed cells that have undergone the transition to generate iPScells. Alternatively, the transformed cells can be cultured underconditions that allow for the production of iPS cells through selectionbased on drug resistance. For example, the transformed vector contains agene that will provide the transformed cells drug resistance (e.g.,blasticidin, zeomycin, hygromycin, or neomycin resistance). Culturinguntransformed cells in media supplemented with the selected drugpromotes cell death. Culturing the transformed cells in mediasupplemented with the selected drug allows for the production of iPScells.

Also provided are methods of producing iPS cells from differentiatedcells comprising transforming the differentiated cells with a firstretroviral vector comprising a loxP site in the 3′ long terminal repeatof the vector and a nucleic acid sequence comprising a nucleic acidsequence encoding an Oct4, a nucleic acid sequence encoding a Sox2, anda nucleic acid sequence encoding a Klf4 (or any of the nucleic acidsequences described above). The nucleic acid sequences are separatedfrom each other by a first and second nucleic acid sequence encoding aviral 2A sequence. The first nucleic acid sequence encoding a viral 2Asequence can be the same as or different from the second nucleic acidsequence encoding a viral 2A sequence. The method further comprisesculturing the transformed cells under conditions that allow for theproduction of an iPS cell. The method can further comprise transformingthe iPS cell with a second vector comprising a nucleic acid sequenceencoding a Cre recombinase. Expression of the Cre recombinase results inthe deletion of the first vector from the genome of the iPS cell, withthe exception of a SIN LTR containing a loxP sequence. Deletion of thefirst vector from the genome of the iPS cell avoids or reduces the riskof insertional mutagenesis caused by the insertion of the vector intothe genome. The method can further comprise isolating a population ofthe iPS cells lacking the first vector. The iPS cells isolated by thismethod are physically different from iPS cells produced by othermethods, as these iPS cells lack the genomically integrated retroviralvector used to create the iPS cell.

Also provided are methods of correcting a genetic mutation of adifferentiated cell prior to producing an iPS cell from thedifferentiated cell. The methods comprise transforming a differentiatedcell with a vector comprising a nucleic acid sequence comprising (i) anucleic acid sequence encoding an Oct4, (ii) a nucleic acid sequenceencoding a Sox2, and (iii) a nucleic acid sequence encoding a Klf4,wherein each of the nucleic acid sequences, (i)-(iii), are separated bya first and second nucleic acid sequence encoding a viral 2A sequence.The vector further comprises a nucleic acid sequence comprising anunmutated nucleic acid sequence of interest and homologous nucleic acidsequences flanking the genetic mutation. Optionally, the vector furthercomprises a first and second loxP sequence. Optionally, the vectorfurther comprises a nucleic acid sequence encoding a Cre recombinaseoperably linked to an inducible promoter. The inducible promoter can,for example, comprise a Nanog-responsive thymidine kinase promoter.Optionally, the vector comprises SEQ ID NO:44.

Optionally, the genetic mutation is a mutation in the nucleic acidsequence encoding β-globin, the nucleic acid sequence encoding cysticfibrosis transmembrane conductance regulator, the nucleic acid sequenceencoding phenylalanine hydroxylase, and/or the nucleic acid sequenceencoding dystrophin.

Optionally, the genetic mutation is a mutation in the nucleic acidsequence encoding β-globin. The mutation in the nucleic acid sequenceencoding β-globin can, for example, result in a glutamic acid to valinesubstitution at the sixth amino acid of the β-globin protein. Theglutamic acid to valine substitution can, for example, be caused by an Ato T transversion at base pair +20 relative to the A(+1) of the ATGstart codon of the nucleic acid sequence encoding β-globin. β-globin isused throughout as an example.

Further provided are iPS cells produced by these methods. iPS cellsproduced by these methods can, for example, be identified based onmorphological characteristics of the cell (e.g., cell shape, cellcomposition, cellular organelle shape, and cell size). An iPS cellproduced by these methods can be identified based on the expression ofES cell markers. ES cell markers can, for example, include Oct3/4,Nanog, E-Ras, Cripto, Dax1, Sox2, Fgf4, stage-specific embryonic antigen1 (SSEA1), SSEA3, SSEA4, alkaline phosphatase, tumor-related antigen(TRA)-1-60, TRA-1-81, and Zfp296. Optionally, an iPS cell produced bythese methods can be identified by comparing CpG methylation patterns ingene promoters of nontransformed, transformed, and ES cells. Optionally,an iPS cell produced by these methods can be identified based on theability to form a teratoma comprised of cells derived from the endoderm,mesoderm, and ectoderm in an immunocompromised mouse. An iPS cell can beidentified by a combination of cell morphological characteristics,expression of ES cell markers, CpG methylation patterns, and the abilityto form a teratoma in an immunocompromised mouse.

Examples of analytical techniques useful in determining the expressionof ES cell markers include reverse transcription-polymerase chainreaction (RT-PCR), quantitative real-time-PCR (qRT-PCR), one step PCR,RNase protection assay, primer extension assay, microarray analysis,gene chip, in situ hybridization, immunohistochemistry, Northern blot,Western blot, enzyme-linked immunosorbent assay (ELISA), enzymeimmunoassay (EIA), radioimmunoassay (RIA), or protein array. Thesetechniques are known. See, e.g., Sambrook et al., Molecular Cloning: ALaboratory Manual, 3^(rd) Ed., Cold Spring Harbor Press, Cold SpringHarbor, N.Y. (2001).

Further provided are kits consisting of any of the first vectorsdescribed and a second vector comprising a nucleic acid sequenceencoding a Cre recombinase. Optionally, the first vector comprises anucleic acid sequence comprising a nucleic acid sequence encoding anOct4, a nucleic acid encoding a Sox2, and a nucleic acid sequenceencoding a Klf4. Each of the nucleic acid sequences are separated by afirst and second viral 2A sequence. The first viral 2A sequence is thesame as or different from the second viral 2A sequence. Optionally,directions to produce an iPS cell from a differentiated cell, a cultureplate for producing the iPS cells, and/or containers for the vector orvectors are included in the kit.

Also provided herein, are methods of treating or preventing a disease ordisorder in a subject at risk of developing a disease or disorder. Themethods comprise isolating differentiated cells from the subject andtransforming the differentiated cells with a first vector comprising anucleic acid comprising a nucleic acid sequence encoding an Oct4, anucleic acid sequence encoding a Sox2, and a nucleic acid sequenceencoding a Klf4. Each of the nucleic acid sequences are separated by afirst and second nucleic acid sequence encoding a viral 2A sequence. Thefirst nucleic acid sequence encoding a viral 2A sequence can be the sameas or different from the second nucleic acid sequence encoding a viral2A sequence. The vector may further comprise a nucleic acid sequencecomprising a therapeutic agent. Alternatively, the transformed cells maybe transformed with a second vector comprising a nucleic acid sequencecomprising a therapeutic agent. The method further comprises isolating apopulation of the iPS cells. The method further comprises administeringto the subject the isolated population of iPS cells that are expressingthe therapeutic agent.

The therapeutic agent can be an RNA molecule, a protein, or a DNAmolecule. An RNA molecule can, for example, comprise an antisense RNAmolecule, a ribozyme, a small interfering RNA (siRNA) that mediates RNAinterference (RNAi), or a microRNA (miRNA) that mediates miRNA-inducedtranslational repression. In the event the therapeutic agent is aprotein, the protein can be a receptor, a signaling molecule, atranscription factor, a factor that promotes or inhibits apoptosis, aDNA replication factor, an enzyme, a structural protein, a neuralprotein, a heat shock protein, or a histone. In the event that thetherapeutic agent is a DNA molecule, the DNA molecule can correct adefective or mutated DNA sequence within the genome of the subject.Ordinary skill in the art determines which therapeutic agents areexpressed to treat a subject with or at risk of developing a disease ordisorder.

Also provided are methods of treating or preventing a disease associatedwith a genetic mutation in a subject. The methods comprise selecting asubject with a disease associated with the genetic mutation; isolatingdifferentiated cells from the subject; transforming the differentiatedcells with a vector comprising an unmutated nucleic acid sequence ofinterest; culturing the transformed cells under conditions that allowfor the production of a population of iPS cells; screening the iPS cellsfor correction of the genetic mutation; and administering an effectiveamount of the iPS cells to the subject. Administration of the iPS cellstreats or prevents the disease associated with the genetic mutation inthe subject. The vector comprising the unmutated nucleic acid sequenceof interest is capable of correcting the genetic mutation associatedwith the disease and is capable of inducing pluripotent stem (iPS)cells. Optionally, the vector comprises a nucleic acid sequencecomprising (i) an unmutated nucleic acid sequence of interest andhomologous nucleic acid sequences flanking the genetic mutation, (ii) anucleic acid sequence encoding a Cre recombinase operably linked to aninducible promoter, (iii) a first and second loxP sequence, (iv) anucleic acid sequence encoding an Oct4, (v) a nucleic acid sequenceencoding a Sox2, and (vi) a nucleic acid sequence encoding a Klf4. Eachof the nucleic acid sequences, (iv)-(vi), are separated by a first andsecond nucleic acid sequence encoding a viral 2A sequence. The firstnucleic acid sequence encoding a viral 2A sequence can be the same as ordifferent from the second nucleic acid sequence encoding a viral 2Asequence. Optionally, the inducible promoter comprises aNanog-responsive thymidine kinase promoter. Optionally, the vectorcomprises SEQ ID NO:44.

Examples of analytical techniques useful in screening an iPS cell forcorrection of the genetic mutation include any DNA-based sequencingassay, reverse transcription-polymerase chain reaction (RT-PCR),quantitative real-time-PCR (qRT-PCR), RNase protection assay, Southernblot, Northern blot, and restriction length polymorphism (RFLP)analysis. These techniques are known. See, e.g., Sambrook et al.,Molecular Cloning: A Laboratory Manual, 3rd Ed., Cold Spring HarborPress, Cold Spring Harbor, N.Y. (2001).

Optionally, administration of the isolated iPS cells to the subject canbe done after the isolated iPS cells have been differentiated tospecific types of stem cells (e.g., hematopoietic stem cells).Administration of the differentiated iPS cells to the subject can bedone systemically (e.g., injection of iPS cells into the circulatorysystem) or it can be localized to an organ or tissue (e.g., injection ofiPS cells or delivery of stem cells, optionally, on or in ascaffold/matrix to specified organ or tissue). Thus, the administerediPS cells are designed so they interact with the tissue or organ or withtarget cells. The method of administration is determined by one of skillin the art to be consistent with the treatment of the disease ordisorder that the subject has or is at risk of developing.

Optionally, the differentiated cell is selected from the groupconsisting of a(n) epithelial cell, keratinocyte, fibroblast,hepatocyte, neuron, osteoblast, myocyte, kidney cell, lung cell, thyroidcell, and pancreatic cell. Optionally, the differentiated cell is akeratinocyte.

The disease associated with a genetic mutation can, for example, beselected from the group consisting of sickle cell disease, thalassemia,cystic fibrosis, phenylketonuria, and Duchenne muscular dystrophy. Thegenetic mutation can be corrected via targeted gene replacement and thedisease is amenable to a gene/cell therapy approach.

As used herein, a subject can be a vertebrate, more specifically amammal (e.g., a human, horse, pig, rabbit, dog, sheep, goat, non-humanprimate, cow, cat, guinea pig or rodent), a fish, a bird or a reptile oran amphibian. The term does not denote a particular age or sex. Thus,adult and newborn subjects, as well as fetuses, whether male or female,are intended to be covered. As used herein, patient or subject may beused interchangeably and can refer to a subject with or at risk ofdeveloping a disease or disorder. The term patient or subject includeshuman and veterinary subjects.

A subject at risk of developing a disease or disorder can be geneticallypredisposed to the disease or condition, e.g., have a mutation in a genethat causes the disease or disorder or have a family history of thedisease or disorder. Additionally, a subject at risk of developing adisease or disorder may have symptoms or signs of early onset for thedisease or condition. A subject with a disease or disorder has one ormore symptoms of the disease or disorder or has been diagnosed with thedisease or disorder.

According to the methods taught herein, the subject is administered aneffective amount of the therapeutic agent and/or iPS cells. The termseffective amount and effective dosage are used interchangeably. The termeffective amount is defined as any amount necessary to produce a desiredphysiologic response. Effective amounts and schedules for administeringthe therapeutic agent and/or iPS cells may be determined empirically,and making such determination is within the skill in the art. The dosageranges for administration are those large enough to produce the desiredeffect in which one or more symptoms of the disease or disorder areaffected (e.g., reduced or delayed). The dosage should not be so largeas to cause substantial adverse side effects, such as unwantedcross-reactions, anaphylactic reactions, and the like. Generally, thedosage will vary with the age, condition, sex, type of disease, theextent of the disease or disorder, route of administration, or whetherother drugs are included in the regimen, and can be determined by one orskill in the art. The dosage can be adjusted by the individual physicianin the event of any contraindications. Dosages can vary, and can beadministered in one or more dose administrations daily, for one orseveral days. Guidance can be found in the literature for appropriatedosages for given classes of pharmaceutical products.

As used herein the terms treatment, treat, or treating refer to a methodof reducing the effects of a disease or condition or one or moresymptoms of the disease or condition. Thus in the disclosed method,treatment can refer to a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or100% reduction in the severity of an established disease or condition orone or more symptoms of the disease or condition. For example, a methodfor treating a disease is considered to be a treatment if there is a 10%reduction in one or more symptoms of the disease in a treated subject ascompared to a control. A control can refer to an untreated subject.Alternatively, a control can comprise samples from the subject prior totreatment (i.e., the levels of one or more symptoms of the disease inthe subject are determined prior to treatment and compared to the levelsof one or more symtpoms of the disease in the subject after treatment).Thus the reduction can be a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%,100%, or any percent reduction in between 10% and 100% as compared tonative or control levels. It is understood that treatment does notnecessarily refer to a cure or complete ablation of the disease,condition, or symptoms of the disease or condition.

As used herein, the terms prevent, preventing, and prevention of adisease or disorder refers to an action, for example, administration ofa therapeutic agent, that occurs before or at about the same time asubject begins to show one or more symptoms of the disease or disorder,wherein the administration inhibits or delays onset or exacerbation ofone or more symptoms of the disease or disorder. As used herein,references to decreasing, reducing, or inhibiting include a change of10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or greater as compared to acontrol level. Such terms can include but do not necessarily includecomplete elimination.

Disclosed are materials, compositions, and components that can be usedfor, can be used in conjunction with, can be used in preparation for, orare products of the disclosed methods and compositions. These and othermaterials are disclosed herein, and it is understood that whencombinations, subsets, interactions, groups, etc. of these materials aredisclosed that while specific reference of each various individual andcollective combinations and permutation of these compounds may not beexplicitly disclosed, each is specifically contemplated and describedherein. For example, if a method is disclosed and discussed and a numberof modifications that can be made to a number of molecules including themethod are discussed, each and every combination and permutation of themethod, and the modifications that are possible are specificallycontemplated unless specifically indicated to the contrary. Likewise,any subset or combination of these is also specifically contemplated anddisclosed. This concept applies to all aspects of this disclosureincluding, but not limited to, steps in methods of using the disclosedcompositions. Thus, if there are a variety of additional steps that canbe performed it is understood that each of these additional steps can beperformed with any specific method steps or combination of method stepsof the disclosed methods, and that each such combination or subset ofcombinations is specifically contemplated and should be considereddisclosed.

Publications cited herein and the material for which they are cited arehereby specifically incorporated by reference in their entireties.

The examples below are intended to further illustrate certain aspects ofthe methods and compositions described herein, and are not intended tolimit the scope of the claims.

EXAMPLES General Methods Production of OSK Polycistronic LentiviralVectors

The complete nucleotide sequence of pKP332 (the OSK polycistroniclentiviral vector) is given by SEQ ID NO:43. The pKP332 vector wasdeposited with the American Type Culture Collection, 10801 UniversityBoulevard, Manassas, Va. 20110-2209 in accordance with the BudapestTreaty on Oct. 6, 2009, and has accession number PTA-10385. The completenucleotide and amino acid map of the polycistron encoded by the vectorused is given by SEQ ID NO:7 (top strand) and SEQ ID NO:9, respectively(FIG. 7). Construction of the polycistron using PTV1 2A sequences andfusion PCR was performed essentially as described (Holst et al., NatureProtocols 1:406-17 (2006)). Briefly, human Oct4 cDNA (Open BiosystemsClone 40125986) (Open Biosystems; Huntsville, Ala.) was PCR amplifiedand modified with primers OCT4-F:cacacagcggccgcatttaaatccaccatggcgggacacctggcttc (SEQ ID NO:10) andOCT4-R: agaggacgaacgaaattgtctctcttcaagcaccgaggcaaacttacgtaccctctcgg (SEQID NO:11) to contain Not I and Swa I restriction sites at the 5′ end anda Kozak consensus sequence. At the 3′ end, the Oct4 stop codon waseliminated and replaced with nucleotides (nt) from PTV 1 2A that willform a 22-nt overlap with the 5′ end of the Sox2 amplicon. Human Sox2cDNA (Open Biosystems Clone 2823424) (Open Biosystems; Huntsville, Ala.)was PCR amplified and modified with primers SOX2-F:ctctgttaaagcaagcaggagatgttgaagaaaaccccgggcctatgtacaacatgatggagacgg (SEQID NO:12) and SOX2-R:agaggacgaacgaaattgtctctcttcaagcaccgaggcctagggtacacactctccccgtcac (SEQ IDNO:13) to overlap with the 3′ end of the Oct4 amplicon and to append 2Ant sequences upstream of the Sox2 ATG. At the 3′ end, the Sox2 stopcodon was eliminated and replaced with nt from PTV 1 2A that will form a22-nt overlap with the 5′ end of the Klf4 amplicon. Human Klf4 cDNA(Open Biosystems Clone 5111134) (Open Biosystems; Huntsville, Ala.) wasPCR amplified and modified with primers KLF4-F:ctctgttaaagcaagcaggagatgttgaagaaaaccccgggcctatggctgtcagcgacgcgc (SEQ IDNO:14) and KLF4-R: gtgtgtcagctgtaaatttaaatttttacggagaagtacacatt (SEQ IDNO:15) to overlap with the 3′ end of the Sox2 amplicon and to append 2Ant sequences upstream of the Klf4 ATG. At the 3′ end, the Klf4 stopcodon was retained and Swa I and Sal I restriction sites were added.After PCR, the individual amplicons were gel purified and used in athree-element fusion PCR at a 1:100:1 (Oct4:Sox2:Klf4) molar ratio alongwith primers OCT4-F (SEQ ID NO:10) and KLF4-R (SEQ ID NO:15) to producea 3623 base pair (bp) amplicon containing the polycistron. Thepolycistron was gel purified and cloned into the general cloning vectorpKP114 using the NotI and SalI restriction sites to produce pKP330 andsequenced for authenticity. Subsequently, the polycistron was removedfrom pKP330 as a Swa I (Roche; Indianapolis, Ind.) fragment andsubcloned into a Swa I site downstream of the EF1α promoter in thelentiviral vector pDL 171 (Levasseur et al., Blood 102:4312-9 (2003)) toproduce the OSK polycistronic lentiviral vector pKP332, which wassequenced for authenticity.

By the same strategy, a second polycistronic lentival vector, pKP333,was produced that substitutes the PTV1 2A peptide between Sox2 and Klf4with the Thosea asigna virus 18 amino acid 2A-like sequence and a GSGlinker (underlined): GSGEGRGSLLT CGDVEENPGP (SEQ ID NO:5).

The complete nucleotide sequence of pKP360 (the OSK polycistroniclentiviral vector designed to correct β-globin mutation) is given by SEQID NO:44. To create this vector, a 6938 base pair (bp)loxP-SalI-NBS-TK-Cre/GFP-EF1a-OCT4-2A-SOX2-2A-KLF4-AscI-loxP DNAfragment is inserted into the second intron of the human β-globin genecontained within a bacterial artificial chromosome (BAC) byrecombineering in DY380 E. coli cells. In a second recombineering step,a capture vector containing an MC1-driven herpes simplex virus thymidinekinase (HSV tk) gene is used to extract a 16,890 bp sequence from theBAC. The captured sequence consists of 5602 bp of human β-globin 5′homology, the 6938 bp insert sequence, and 4350 bp of human β-globin 3′homology. The first and second β-globin exons are contained within the5′ homology and the third exon is contained within the 3′ homology.pKP360 contains a unique NotI restriction site at nucleotide #21049 forvector linearization prior to transfection. The HSV tk gene is used as anegative selection marker for random integration of the vector. Briefly,following transfection with pKP360 of differentiated cells isolated froma sickle cell disease (SCD) patient, 3 classes of cells results: (1)cells that do not receive the vector; these cells remain differentiatedand eventually die in culture due to a limited replicative life span;(2) cells that integrate the vector in a non-targeted location; thesecells could become iPS cells but will be selected against by gancyclovirbecause they contain the HSV tk gene; and (3) cells that integrate thevector by homologous recombination into the β-globin locus; these cellshave lost the HSV tk marker and will therefore survive gancyclovirselection to become iPS cells with a corrected β-globin gene.

PCR reactions were performed using PrimeStar polymerase (Takara BioInc.; Otsu, Shiga, Japan). All of the oligos used in this study weresynthesized by Integrated DNA Technologies (IDT; Coralville, Iowa) andall DNA gel extractions were performed using QIAquick Gel ExtractionKits (Qiagen; Valencia, Calif.).

Cell Culture and Viral Infections

Embryonic stem (ES) and induced pluripotent stem (iPS) cells werecultured on irradiated murine embryonic fibroblasts (MEFs) in ES cellmedia consisting of DMEM supplemented with 1× non-essential amino acids,1× penicillin-streptomycin, 1× L-glutamine (Mediatech; Manassas, Va.),1× nucleosides (Chemicon; Temecula, Calif.), 15% Fetal Bovine Serum(FBS) (Hyclone; Logan, Utah), 2-ME (Sigma; St. Louis, Mo.) and LeukemiaInhibitory Factor (LIF) (laboratory preparation).

For preparation of lentivirus, 140 μg of the polycistronic vector(pKP332), 70 μg of the envelope plasmid (pMDG), and 105 μg of thepackaging plasmid (pCMBVdR8.9.1) were co-transfected into 1.7×10⁷ 293Tcells by the CaCl₂ method as previously described (Levasseur et al.,Blood 102:4312-9 (2003)). Virus-containing supernatant was collected 2days after transfection, passed through a 0.45 μm filter andconcentrated by centrifugation at 26,000 rpm for 90 minutes at 8° C. inan SW-28 rotor using a Beckman XL-100 ultracentrifuge (Beckman;Fullerton, Calif.).

For iPS cell induction, 3×10⁵ mouse tail-tip fibroblasts (TTFs) wereseeded onto one well of a 6-well plate. The next day, 2.5 μL of theconcentrated virus was mixed with 2 mL of ES cell medium containing 8μg/mL polybrene and added to the TTFs. Forty-eight hours later, the TTFswere trypsinized and transferred to a 100 mm dish without MEFs andcontinuously cultured on the same dish for 3 weeks with daily mediachanges. Potential iPS cell colonies started to appear after 2-3 weeks.These colonies were individually picked and expanded on MEFs foranalysis.

To remove the integrated lentiviral and polycistronic sequences, iPScells were either electroporated with a Cre-expressing plasmid(pCAGGS-Cre) or infected with a Cre-expressing adenovirus (rAd-Cre-IE).Individual colonies were picked and Cre-mediated removal of floxedsequences was verified by PCR and southern blot analysis.

For the construction of rAd-Cre-IE (rAd-Cre-IRES-EGFP), Cre cDNA was PCRamplified from pCAGGS-Cre and inserted between the NheI and EcoRI sitesof the expression vector pEC-IE, which contains an IRES-EGFP downstreamof the MCS. The Cre-IE expression cassette is flanked by attL1 and attL2sites, thus allowing transfer of the Cre-IE sequence from pEC-IE topAd/p1-DEST (Invitrogen; Carlsbad, Calif.) by the LR reaction. Therecombinant adenovirus was packaged in 293A cells according to themanufacturer's instructions.

Primary human keratinocytes were isolated from a patient skin biopsy.Briefly, the biopsied tissue was placed into Keratinocyte-SFM (9K-SFM;Invitrogen; Carlsbad, Calif.) supplemented with 10 mg/ml Dispase and 2×Antibiotics/Antimycotics (CELLnTEC CnT-ABM) and incubated overnight at4° C. The next day, the keratinocyte-containing epidermal layer wasisolated from the fibroblast-containing dermal layer with forceps andthen trypsinized for 20 minutes at room temperature. Cell clumps weretriturated with a pipet and then centrifuged at 200×g for 5 minutes.Cells were resuspended in K-SFM and 1× Antibiotics/Antimycotics,transferred to one well of a six-well plate, and incubated at 37° C.with daily media changes. For transduction, 3×10⁵ keratinocytes wereseeded into one well of a six-well plate in K-SFM. The next day themedia was removed and replaced with 2 ml of K-SFM containing 5 mg/ml ofpolybrene and the polycistronic lentivirus. After 24 hours, thetransduced cells were trypsinized, centrifuged, resuspended in K-SFM andtransferred into a 10 cm tissue culture dish containing γ-irradiatedCF-1 murine embryonic fibroblasts (MEFs). The next day, the medium waschanged to human ES cell medium (DMEM/F-12, 20% Knockout SR, 2 mML-glutamine, 1× Pen/Strep, 1× nonessential amino acids (all fromInvitrogen; Carlsbad, Calif.), 0.5 mM β-mercaptoethanol (Sigma; St.Louis, Mo.), and 4 ng/ml bFGF (Calbiochem; San Diego, Calif.)). Cellswere incubated at 37° C. with daily media changes and after 10 days,CF-1 conditioned medium was added. iPS colonies appeared after about 30days.

With the exception of the pKP332 construction, all of the PCRs performedused ExTaq polymerase (Takara Bio Inc.; Otsu, Shiga, Japan). All of thesequencing was performed by the Genomics Core Facility of the Howell andElizabeth Heflin Center for Human Genetics of the University of Alabamaat Birmingham using the BigDye Terminator v3.1 Cycle Sequencing ReadyReaction kit as per the manufacture's instructions (Applied Biosystems;Foster City, Calif.). The sequencing products were run followingstandard protocols on an Applied Biosystems 3730 Genetic Analyzer withPOP-7 polymer.

Immunostaining and AP Staining

iPS cells were cultured on cover slips pretreated with FBS, fixed with4% paraformaldehyde and permeabilized with 0.5% Triton X-100. Cells werestained with DAPI and primary antibodies against Nanog and SSEA1 (R&DSystems; Minneapolis, Minn.) and incubated with fluorophore-labeledsecondary antibodies (Jackson Immunoresearch; West Grove, Pa.).

For AP staining, 100-200 iPS cells were seeded onto one well of asix-well plate and cultured for one week. iPS cells were then stainedusing the Vector Blue Alkaline Phosphatase Substrate Kit III (VectorLaboratories; Burlingame, Calif.) according to the manufacturer'sinstructions.

RT-PCR Analysis

Total RNA was isolated from cells with Trizol reagent (Invitrogen;Carlsbad, Calif.). RNA was pretreated with RQ1 RNase-free DNase(Promega; Madison, Wis.) and reverse transcribed with SuperScriptFirst-Strand Synthesis System (Invitrogen; Carlsbad, Calif.) using oligod(T)n. Primers for PCR amplification of the cDNA were: polycistronictransgene F, gatgaactgaccaggcacta (SEQ ID NO:16) and polycistronictransgene R, gattatcggaattccctcgag (SEQ ID NO:17); Nanog F,accaaaggatgaagtgcaag (SEQ ID NO:18) and Nanog R, agttttgctgcaactgtacg(SEQ ID NO:19); Oct4 F, agcttgggctagagaaggat (SEQ ID NO:20) and Oct4 R,tcagtttgaatgcatgggag (SEQ ID NO:21); Sox2 F, tgcacatggcccagcacta (SEQ IDNO:22) and Sox2 R, ttctccagttcgcagtccag (SEQ ID NO:23); Cripto F,aacttgctgtctgaatggag (SEQ ID NO:24) and Cripto R, tttgaggtcctggtccatca(SEQ ID NO:25); Klf4 F, cagcagggactgtcaccctg (SEQ ID NO:26) and Klf4 R,ggtcacatccactacgtgggat (SEQ ID NO:27); and Natl F, ggagagtgcgattgcagaag(SEQ ID NO:28) and Natl R, ggtcacatccactacgtggga (SEQ ID NO:29).

Bisulfite Modification and Sequencing

Bisulfite treatment of DNA was performed with the CpGenome Fast DNAModification Kit (Chemicon; Temecula, Calif.) according to themanufacturer's instructions. The Oct4 and Nanog gene promoter regionswere amplified by nested PCR using the Oct4 primers F1,gttgttttgttttggttttggatat (SEQ ID NO:30), Oct4 F2,atgggttgaaatattgggtttattta (SEQ ID NO:31) and Oct4 R,ccaccctctaaccttaacctctaac (SEQ ID NO:32) or the Nanog primers F1,gaggatgttttttaagtttttttt (SEQ ID NO:33), Nanog F2,aatgtttatggtggattttgtaggt (SEQ ID NO:34) and Nanog R,cccacactcatatcaatataataac (SEQ ID NO:35). Amplified PCR products werepurified using a QIAgen Gel Extraction Kit (Qiagen; Valencia, Calif.),cloned into a Topo TA vector (Invitrogen; Carlsbad, Calif.), andsequenced with T7 and Ml3R primers.

Southern Blot Analysis

Ten μg of genomic DNA were digested with BamHI or KpnI (Roche;Indianapolis, Ind.), separated on a 0.8% agarose gel and blotted ontoHybond-N⁺ membrane (Amersham Biosciences; Piscataway, N.J.). Thepolycistronic vector served as template to PCR amplify a 0.3 kb SIN LTRprobe using the primers SIN LTR F, gctcggtacctttaagaccaatgac (SEQ IDNO:36) and SIN LTR R, atgctgctagagattttccacactg (SEQ ID NO:37). Toproduce the internal probe, the polycistronic vector was digested withSalI and XhoI (Roche; Indianapolis, Ind.) and the 1 kb fragmentcontaining the EF1α promoter was gel purified. Probes were labeled usingthe Random Primed DNA Labeling Kit (Roche; Indianapolis, Ind.) with³²P-α-dCTP and blots were hybridized in MiracleHyb solution (Stratagene;La Jolla, Calif.).

Inverse PCR

One to two μg of total genomic DNA were digested with thetetranucleotide-recognizing restriction enzymes MseI or AluI (NewEngland Biolabs (NEB); Ipswich, Mass.). The digested fragments werediluted and incubated with T4 DNA Ligase (Roche; Indianapolis, Ind.) toobtain self-ligated monomers, which were then linearized with thehexanucleotide-recognizing restriction enzymes NcoI or XmnI (NEB;Ipswich, Mass.). These fragments were isolated by ethanol precipitationand used as templates in PCR reactions using the primers 5LentiR1,tgaattgatcccatcttgtcttcg (SEQ ID NO:38) and SLentiF1,tgctgctttttgcttgtactgg (SEQ ID NO:39). PCR products were run on a 2%agarose gel in the presence of ethidium bromide (0.5 μg/mL). All bandsvisible under UV light were gel purified and sequenced.

Teratoma Formation

One million iPS cells in a 100 μL volume of PBS were injected via a 21 Gneedle into the dorsal flanks of SCID mice. Teratomas were recovered 4-5weeks postinjection and processed for histological analysis.

Production and Analysis of Chimeric Mice

C57BL/6 blastocysts were injected with iPS cells and then transferred topseudopregnant CD-1 females. After two weeks, embryos were collected forphotographs and analyzed for chimerism using PCR. Embryos wereindividually minced and lysed overnight at 55° C. in a solution ofProteinase K and SDS. DNA was then purified from the lysate byphenol/chloroform extraction and ethanol precipitation. PCR wasperformed using the primers mbeta KI F, ttgagcaatgtggacagagaagg (SEQ IDNO:40), mbeta KI R, gtcagaagcaaatgtgaggagca (SEQ ID NO:41) and 1400gammaR, aattctggcttatcggaggcaag (SEQ ID NO:42).

Example 1 iPS Cells Produced by Transduction of Polycistronic Oct4,Sox2, Klf4 (OSK) Vector

FIG. 1A illustrates the lentiviral vector constructed for transductionof adult skin fibroblasts. Human Oct4, Sox2 and Klf4 cDNAs (OSK) werelinked with porcine teschovirus-1 (PTV1) 2A sequences that function ascis-acting hydrolase elements (CHYSELs) to trigger ribosome skipping(Donnelly et al., J. Gen. Virol. 82:1013-25 (2001); Chinnasamy et al.,Virol. J. 3:14 (2006)). The 2A peptide sequences (FIG. 1B) are cleavedduring translation and produce Oct4 and Sox2 proteins containing anadditional 21 amino acids at the carboxy-termini. A single proline isalso appended to the amino-termini of Sox2 and Klf4. The OSK polycistronwas subcloned downstream of an EF1α promoter in a self-inactivating(SIN) lentiviral vector containing a loxP site in the truncated 3′ LTR(Zuffferey et al., J. Virol. 72:9873-80 (1998); Levasseur et al., Blood102:4312-9 (2003)). After lentivirus production, one million adult skinfibroblasts derived from tail tips of humanized sickle mice weretransduced with the polycistronic vector, and four colonies with highlydefined borders and tightly packed cells were picked at 19 to 30 dayspost-transduction. These colonies were expanded and stained for alkalinephosphatase, Nanog and SSEA1, which are characteristic markers ofpluripotent stem cells. FIGS. 2A and 2B illustrate the staining patternof typical colonies (iPS-1 and iPS-2). The colonies stained intenselyfor alkaline phosphatase and strongly with antibodies to Nanog andSSEA1.

Reverse transcription-polymerase chain reaction (RT-PCR) assays forexpression of additional iPS cell markers are shown in FIG. 3A. iPS-1,-2, and -3 cells expressed polycistronic OSK RNA and endogenous Oct4,Sox2, Klf4, Nanog and Cripto RNA (FIG. 3A). Consistent with theseresults, bisulfite sequencing of the endogenous Oct4 and Nanog promotersin iPS-1 and iPS-2 cells demonstrated effective demethylation of thesesequences (FIG. 3B). CpGs in the endogenous Oct4 and Nanog promoters oftail tip fibroblasts (TTFs) were highly methylated (FIG. 3B) andendogenous Oct4, Sox2, Nanog and Cripto RNAs were not detected (FIG.3A).

When these iPS cells were injected into the dorsal flanks of nonobesediabetic (NOD)/SCID IL-2 γR−/−mice, teratomas containing tissue derivedfrom all three germ layers were obtained (FIG. 5A). These resultsdemonstrate that the polycistronic OSK lentiviral vector effectivelyreprograms adult skin fibroblasts to induced pluripotent stem cells.

Example 2 Removal of Polycistronic OSK Vector from iPS Cell Genome byExogenous Cre Recombinase Expression

The polycistronic vector was deleted by electroporation of iPS cellswith a Cre recombinase-expressing plasmid or by infection of iPS cellswith adenovirus that expresses Cre recombinase (Adeno/Cre).Subsequently, individual colonies were picked, expanded and iPS cell DNAwas analyzed by Southern blot hybridization (FIG. 4B). DNA isolatedbefore (iPS-1) and after (iPS-1 Cre) Cre expression was digested withKpn I, which cuts once within the OSK polycistron, and probed with a DNAfragment containing EF1α sequences. Four bands are observed for iPS-1DNA indicating that four copies of the polycistronic OSK vector areintegrated into the genome (also see FIG. 6B, iPS-2 cells contain 3copies of the vector). None of these four bands are observed in iPS-1Cre DNA; only a band representing endogenous EF1α sequences is detected.These results demonstrate that transient Cre expression effectivelydeletes all copies of the polycistronic OSK lentiviral vector.

Junctions of the four iPS-1 insertion sites were cloned by inverse PCRand sequenced (Pawlik et al., Gene 165:173-81 (1995); Silver andKeerikatte, J. Virol. 63:1924-8 (1989)). Table 2 lists the locations ofthese sites. Three of the insertion sites are within introns, and one islocated in an intergenic region that is 2 megabases (Mb) downstream ofthe transcription start site (TSS) of the NMBr gene and 1 Mb upstream ofthe TSS of the Cited2 gene. These results demonstrate that iPS cells canbe readily obtained by this procedure without interruption of codingsequences, promoters or known regulatory elements. Cloning andsequencing of the insertion sites from iPS-1 Cre cells demonstrated thatonly the 291 base pair (bp) 3′ LTR of the polycistronic vector remainsin the genome. This small SIN LTR does not contain a promoter orenhancer; therefore, the probability of insertional activation orinactivation of endogenous genes is low.

TABLE 2 OSK lentiviral integration sites. iPS Clones No: Chrom. GeneName Gene ID Location Base from TSS iPS-1 1 CH2 RAB14 MGI:1915615 Intron+8,129 2 CH8 Cadherin 13 MGI:99551 Intron +24,738 3 CH10Cbp/p300-interacting MGI:1306784 Intergenic −966,513 transactivator 4CH14 F-box protein 34 MGI:1926188 Intron +52,366 iPS-2 1 CH5 RibokinaseMGI:1918586 Intron +38,503 2 CH15 Estrogen receptor-binding MGI:1859920Intron +20,439 fragment associated gene 9 3 CH15 Angiopoietin 1MGI:108448 Intron +21,069

FIGS. 2A and 2B demonstrate that iPS-1 Cre cells continue to stainpositive for alkaline phosphatase, Nanog and SSEA1 after OSK deletion,and FIG. 3A demonstrates that expression of endogenous Oct4, Sox2, Klf4,Nanog and Cripto was maintained in the absence of OSK expression. Asexpected, the endogenous Oct4 and Nanog promoters remained demethylatedafter OSK deletion (FIG. 3B).

Finally, two iPS-1 Cre cell lines were injected into wild-typeblastocysts, and these blastocysts were transferred into the uteri ofpseudo-pregnant female mice. After two weeks, embryos were analyzed forchimerism by PCR with primers specific for human and mouse β-globingenes. FIG. 5B demonstrates that several high-level chimeras wereobtained; most tissues of these embryos were derived from iPS-1 Crecells which contain only human β-globin genes. One pregnancy was allowedto proceed to term, and FIG. 5C shows an adult high-level chimera(right) derived from iPS-1 Cre 2 cells. These results demonstrate thatadult skin fibroblasts can be effectively reprogrammed to iPS cells withthe polycistronic lentiviral vector and that tissues from all three germlayers can be derived from these cells.

Example 3 iPS Cells Derived from Human Keratinocytes

To determine whether iPS cells were produced from primary humankeratinocytes, primary human keratinocytes were cultured from a patientskin biopsy. The cultured cells were transduced with the vectordescribed above. After 24 hours, the transduced cells were trypsinized,centrifuged, resuspended in media and transferred into a tissue culturedish containing murine embryonic fibroblasts (MEFs). After about 30 daysin culture, iPS colonies were produced. The iPS cells from the humankeratinocytes were sustainable in culture and were capable of multiplepassages. FIG. 8 shows a brightfield image of one of the iPS cellcolonies produced. The iPS cell colony was stained with SSEA-4, which isan antibody that recognizes human embryonic stem cells, but notdifferentiated cells, to confirm the presence of embryonic stem cellscomprising the iPS cell colony. The same iPS colony was stained withDAPI, which is a general nuclear stain, to confirm the presence ofnuclei in the cells of the iPS cell colony.

Example 4 Correction of Sickle Cell Disease (SCD) with ConcomitantFormation of iPS Cells

FIG. 9 shows a schematic of a method to correct a β^(s)-globin mutationin a cell from a subject with sickle cell disease (SCD) whilededifferentiating the cell to a pluripotent state. The method isapplicable to a range of genetic mutations.

To determine whether the β-globin locus of a subject with SCD iscorrected, cells from a human subject with SCD are collected andexpanded in culture. The mutated β^(s)-globin locus is depicted at thetop of FIG. 9. The β^(s)-globin mutation is a single nucleotide, A to Ttransversion, that changes the normal GAG codon to a GTG codon in exon 1of β-globin. As a result, the sixth amino acid of the β^(s)-globin is avaline instead of the normal glutamic acid.

Once the cells are expanded in culture, the targeting vector (middle ofFIG. 9) is introduced into the cells from the subject with SCD. Thevector contains the normal GAG nucleotide sequence in the first exon andflanking sequences to effect homologous recombination within the targetlocus. A herpes simplex virus thymidine kinase (HSV tk) gene is locatedoutside of the sequences used to effect homologous recombination.Integrated between the flanking homology arms is a floxed cassetteconsisting of a Nanog-responsive thymidine kinase promoter drivingexpression of a Cre recombinase and the EF1α promoter driving expressionof the Oct4-Sox2-Klf4 polycistronic sequence. Alternatively, the floxedcassette can contain a marker gene that can either be an addition to thepolycistron or have its own promoter. The marker can be used as apositive selection to select cells that have incorporated the vector.

The targeting vector homologously recombines with the mutatedβ^(s)-globin locus incorporating the corrected GAG codon. TheOct4-Sox2-Klf4 polycistron is expressed, resulting in thededifferentiation of the cells. While Oct4, Sox2, and Klf4 are expressedfrom the EF1α promoter, the TK promoter remains silent. Once the cellbegins to dedifferentiate, the endogenous Nanog gene is expressed.Expression of Nanog results in the activation of the TK promoter, whichis Nanog responsive. Activation of the TK promoter results in theexpression of Cre recombinase. Cre recombinase binds to the loxP sitesto effect the deletion of the floxed cassette, resulting in a correctedβ-globin locus containing a single loxP site in between the second andthird exons of the corrected β-globin locus (bottom of FIG. 9). Excisionof the floxed cassette is important for two reasons: (1) it prevents thedisregulation of the corrected β-globin gene, and (2) it halts theexpression of the vector-introduced reprogramming factors, as theircontinued expression inhibits the reprogramming process.

1. A method of producing an induced pluripotent stem (iPS) cell from adifferentiated cell comprising transforming the differentiated cell witha first vector, wherein the first vector comprises a nucleic acidsequence comprising (i) a nucleic acid sequence encoding an Oct4, (ii) anucleic acid sequence encoding a Sox2, and (iii) a nucleic acid sequenceencoding a Klf4, wherein each of the nucleic acid sequences, (i)-(iii),are separated by a first and second nucleic acid encoding a viral 2Asequence.
 2. The method of claim 1, wherein the vector comprises SEQ IDNO:7.
 3. The method of claim 1, wherein the vector comprises a nucleicacid sequence encoding SEQ ID NO:9.
 4. The method of claim 1, furthercomprising culturing the transformed cell under conditions that allowfor the production of a population of iPS cells.
 5. The method of claim1, further comprising isolating the population of iPS cells. 6.(canceled)
 7. (canceled)
 8. (canceled)
 9. (canceled)
 10. (canceled) 11.(canceled)
 12. The method of claim 1, wherein the differentiated cell isa mammalian cell.
 13. The method of claim 12, wherein the mammalian cellis a human cell.
 14. The method of claim 13, wherein the mammalian cellis selected from the group consisting of a(n) epithelial cell,keratinocyte, fibroblast, hepatocyte, neuron, osteoblast, myocyte,kidney cell, lung cell, thyroid cell, and pancreatic cell.
 15. Themethod of claim 14, wherein the mammalian cell is a keratinocyte. 16.(canceled)
 17. (canceled)
 18. (canceled)
 19. The method of claim 1,wherein the first and second nucleic acid sequences encoding a viral 2Asequence comprises a nucleic acid sequence encoding the amino acidsequence ATNFSLLKQAGDVEENPGP (SEQ ID NO:2) or EGRGSLLTCGDVEENPGP (SEQ IDNO:3).
 20. The method of claim 1, wherein the first nucleic acidsequence encoding a viral 2A sequence comprises a nucleic acid sequenceencoding the amino acid sequence ATNFSLLKQAGDVEENPGP (SEQ ID NO:2) andthe second nucleic acid sequence encoding a viral 2A sequence comprisesa nucleic acid sequence encoding the amino acid sequenceEGRGSLLTCGDVEENPGP (SEQ ID NO:3).
 21. The method of claim 1, wherein thefirst vector is a plasmid, an adenoviral vector or a retroviral vector.22. The method of claim 21, wherein the retroviral vector is alentiviral vector.
 23. The method of claim 22, wherein the lentiviralvector is a lentiviral SIN vector.
 24. The method of claim 21, whereinthe retroviral vector comprises a 3′ long terminal repeat.
 25. Themethod of claim 24, wherein the retroviral vector further comprises aloxP sequence.
 26. The method of claim 25, wherein the loxP sequence isin a 3′ long terminal repeat of the lentiviral vector.
 27. The method ofclaim 25, further comprising transforming the iPS cell with a secondvector, wherein the second vector comprises a nucleic acid encoding aCre recombinase, wherein expression of the Cre recombinase results inthe deletion of the first vector from the genome of the iPS cells. 28.The method of claim 27, further comprising isolating a population of iPScells lacking the first vector.
 29. An isolated iPS cell produced by themethod described in claim
 28. 30. The method of claim 1, furthercomprising correcting a genetic mutation in the differentiated cell,wherein the first vector further comprises a nucleic acid sequencecomprising an unmutated nucleic acid sequence of interest and homologousnucleic acid sequences flanking the genetic mutation to be corrected.31. The method of claim 30, wherein the genetic mutation is a mutationin the nucleic acid sequence encoding β-globin, the nucleic acidsequence encoding cystic fibrosis transmembrane conductance regulator,the nucleic acid sequence encoding phenylalanine hydroxylase, and thenucleic acid sequence encoding dystrophin.
 32. The method of claim 31,wherein the genetic mutation is a mutation in the nucleic acid sequenceencoding β-globin.
 33. The method of claim 32, wherein the mutation inthe nucleic acid sequence encoding β-globin results in a glutamic acidto valine substitution at the sixth amino acid of the β-globin protein.34. The method of claim 33, wherein the glutamic acid to valinesubstitution is caused by an A to T transversion at base pair +20relative to the A(+1) of the ATG start codon of the nucleic acidsequence encoding β-globin.
 35. The method of claim 30, wherein thefirst vector further comprises a first and second loxP sequence.
 36. Themethod of claim 35, wherein the first vector further comprises a nucleicacid sequence encoding a Cre recombinase operably linked to an induciblepromoter.
 37. The method of claim 36, wherein the inducible promotercomprises a Nanog-responsive thymidine kinase promoter.
 38. The methodof claim 30, wherein the first vector comprises SEQ ID NO:44. 39-70.(canceled)
 71. A method of treating or preventing a disease associatedwith a genetic mutation in a subject, the method comprising: (a)selecting a subject with a disease associated with a genetic mutation;(b) isolating differentiated cells from the subject; (c) transformingthe differentiated cells with a vector comprising an unmutated nucleicacid sequence of interest; (d) culturing the transformed cells underconditions that allow for the production of a population of iPS cells;(e) screening the iPS cells for correction of the genetic mutation; and(f) administering the iPS cells to the subject, wherein administrationof the iPS cells treats or prevents the disease associated with thegenetic mutation in the subject.
 72. The method of claim 71, wherein thevector comprises a nucleic acid sequence comprising (i) an unmutatednucleic acid sequence of interest and homologous nucleic acid sequencesflanking the genetic mutation, (ii) a nucleic acid sequence encoding aCre recombinase operably linked to an inducible promoter, (iii) a firstand second loxP sequence, (iv) a nucleic acid sequence encoding an Oct4,(v) a nucleic acid sequence encoding a Sox2, and (vi) a nucleic acidsequence encoding a Klf4, wherein each of the nucleic acid sequences,(iv)-(vi), are separated by a first and second nucleic acid sequenceencoding a viral 2A sequence.
 73. The method of claim 72, wherein theinducible promoter comprises a Nanog-responsive thymidine kinasepromoter.
 74. The method of claim 71, wherein the disease caused by themutation in the genome is selected from the group consisting of sicklecell disease, thalassemia, cystic fibrosis, phenylketonuria, andDuchenne muscular dystrophy.
 75. The method of claim 74, wherein thedisease is sickle cell disease.
 76. The method of claim 75, wherein thevector comprises SEQ ID NO:44.
 77. The method of claim 71, wherein thedifferentiated cell is selected from the group consisting of a(n)epithelial cell, keratinocyte, fibroblast, hepatocyte, neuron,osteoblast, myocyte, kidney cell, lung cell, thyroid cell, andpancreatic cell.
 78. The method of claim 77, wherein the differentiatedcell is a keratinocyte.